def __init__(self,
gl_widget,
projection_file=None,
simmx_file=None,
particle_file=None):
self.init_lock = True # a lock indicated that we are still in the __init__ function
self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
EM3DSymModel.__init__(self, gl_widget)
self.window_title = "SimmxXplor"
#InputEventsManager.__init__(self)
self.projection_file = projection_file # a projection file produced by e2project3d
self.particle_file = particle_file # A file containing particles to be examined
self.current_particle = -1 # keep track of the current particle
self.current_projection = None # keep track of the current projection
self.ptcl_display = None # display all particles
self.mx_display = None # mx display module for displaying projection and aligned particle
self.lay = None # 2d plot for displaying comparison between particle and projection
self.simcmp = "dot:normalize=1"
self.align = "rotate_translate_flip"
self.aligncmp = "dot"
self.refine = "refine"
self.refinecmp = "dot:normalize=1"
self.shrink = 1
def __init__(self, gl_widget, projection_file=None,simmx_file=None,particle_file=None): self.init_lock = True # a lock indicated that we are still in the __init__ function self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study EM3DSymModel.__init__(self, gl_widget) self.window_title = "SimmxXplor" self.projection_file = projection_file # a projection file produced by e2project3d self.simmx_file = simmx_file # a similarity matrix produced by e2simmx or by e2classaverage - should have the same number of columns (nx) as the number of projections self.particle_file = particle_file # a similarity matrix produced by e2simmx or by e2classaverage - should have the same number of columns (nx) as the number of projections self.num_particles = None # keep track of the total number of particles ( the y dimension of the simmx file) self.current_particle = 0 # keep track of the current particle self.current_projection = None # keep track of the current projection self.projections = None # a list of the projections - the initial design keeps them all in memory - this could be overcome self.mx_display = None # mx display widget for displaying projection and aligned particle self.frc_display = None # 2d plot for displaying comparison between particle and projection self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis
def __init__(self,
gl_widget,
projection_file=None,
simmx_file=None,
particle_file=None):
self.init_lock = True # a lock indicated that we are still in the __init__ function
self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
EM3DSymModel.__init__(self, gl_widget)
self.window_title = "SimmxXplor"
self.projection_file = projection_file # a projection file produced by e2project3d
self.simmx_file = simmx_file # a similarity matrix produced by e2simmx or by e2classaverage - should have the same number of columns (nx) as the number of projections
self.particle_file = particle_file # a similarity matrix produced by e2simmx or by e2classaverage - should have the same number of columns (nx) as the number of projections
self.num_particles = None # keep track of the total number of particles ( the y dimension of the simmx file)
self.current_particle = 0 # keep track of the current particle
self.current_projection = None # keep track of the current projection
self.projections = None # a list of the projections - the initial design keeps them all in memory - this could be overcome
self.mx_display = None # mx display widget for displaying projection and aligned particle
self.frc_display = None # 2d plot for displaying comparison between particle and projection
self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis
def __init__(self, gl_widget, projection_file=None,simmx_file=None,particle_file=None): self.init_lock = True # a lock indicated that we are still in the __init__ function self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study EM3DSymModel.__init__(self,gl_widget) self.window_title = "SimmxXplor" #InputEventsManager.__init__(self) self.projection_file = projection_file # a projection file produced by e2project3d self.particle_file = particle_file # A file containing particles to be examined self.current_particle = -1 # keep track of the current particle self.current_projection = None # keep track of the current projection self.ptcl_display = None # display all particles self.mx_display = None # mx display module for displaying projection and aligned particle self.lay = None # 2d plot for displaying comparison between particle and projection self.simcmp = "dot:normalize=1" self.align = "rotate_translate_flip" self.aligncmp = "dot" self.refine = "refine" self.refinecmp = "dot:normalize=1" self.shrink=1
def __init__(self, gl_widget=None, auto=True,sparse_mode=False, file_name = ""):
self.current_hit = None
self.events_mode_list = ["navigate", "inspect"]
self.events_mode = self.events_mode_list[1]
self.init_lock = True # a lock indicated that we are still in the __init__ function
self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
if auto: # this a flag that tells the eulerxplorer to search for refinement data and automatically add elements to the inspector, if so
self.gen_refinement_data()
EM3DSymModel.__init__(self, gl_widget, eulerfilename=file_name)
Animator.__init__(self)
self.height_scale = 8.0 # This is a value used in EM3DSymModel which scales the height of the displayed cylinders - I made it 8 because it seemed fine. The user can change it anyhow
self.projection_file = None # This is a string - the name of the projection images file
self.average_file = None # This is a string - the name of the class averages file
self.proj_class_viewer = None # This will be an EMImageMXWidget that shows the class and/or projection
self.particle_viewer = None # This will be an EMImageMXWidget that shows the particles in a class
self.clsdb = None # I think this will become redundant - it used to be the old database that stores which particles are in a class, but now that's stored in the header
self.particle_file = None # This will be a string - the name of the file that has the particle files in it. This might be made redundant with the new approach
self.alignment_file = None # This will be a string - the name of the file containing the alignment parameters - this is essential if you we want to show the aligned particles
self.refine_dir = None # This will be a string - the name of the current refinement directory that is being studied
self.dx = None # This is an EMData object storing the x shifts of the alignments for all particles. Generated by e2classaverage
self.dy = None # This is an EMData object storing the y shifts of the alignments for all particles. Generated by e2classaverage
self.da = None# This is an EMData object storing the angle of the alignments for all particles. Generated by e2classaverage
self.dflip = None # This is an EMData object storing whether or not tthe alignment involved a flip, for all particles. Generated by e2classaverage
self.classes = None # This is an EMData object storing which class(es) a particle belongs to. Generated by e2classaverage
self.inclusions = None # This is and EMDAta storing a boolean that indicates the particle was actually included in the final average. Generated by e2classaverage
self.average = None # This the class average itself, an EMData object
self.projection = None # This is the projection itelse, an EMData object
self.class_idx = None # This is the idx of the current class being studied in the interface
self.previous_len = -1 # To keep track of the number of class averages that were previously viewable. This helps to make sure we can switch to the same class average in the context of a different refinement iteration
self.mirror_eulers = False
if sparse_mode:
self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis
# Grab the symmetry from the workflow database if possible
sym = "c1"
if js_check_dict("refine_01/0_refine_parms.json"):
try: sym = str(js_open_dict("refine_01/0_refine_parms.json")["sym"])
except: pass
# Have to tell the EM3DSymModel that there is a new sym
self.set_symmetry(sym)
# this object will have
if self.au_data != None:
combo_entries = self.au_data.keys()
combo_entries.sort()
combo_entries.reverse()
if len(combo_entries) > 0:
au = combo_entries[0]
cls = self.au_data[au][0][0]
self.au_selected(au,cls)
self.mirror_eulers = True
self.init_lock = False
self.force_update=True # Force a display udpdate in EMImage3DSymModule
QtCore.QObject.connect(self, QtCore.SIGNAL("point_selected"), self.au_point_selected)
def __init__(self, gl_widget=None, auto=True,sparse_mode=False, file_name = "", read_from=None):
self.current_hit = None
self.events_mode_list = ["navigate", "inspect"]
self.events_mode = self.events_mode_list[1]
self.init_lock = True # a lock indicated that we are still in the __init__ function
self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
if len(read_from)==0:
read_from=None
self.readfrom=read_from
if self.readfrom:
file_name=""
auto=False
datalst=[]
for rr in self.readfrom:
datalst.append([rr,None, None, None,rr])
self.au_data={"data":datalst}
if auto: # this a flag that tells the eulerxplorer to search for refinement data and automatically add elements to the inspector, if so
self.gen_refinement_data()
EM3DSymModel.__init__(self, gl_widget, eulerfilename=file_name)
Animator.__init__(self)
self.height_scale = 8.0 # This is a value used in EM3DSymModel which scales the height of the displayed cylinders - I made it 8 because it seemed fine. The user can change it anyhow
self.projection_file = None # This is a string - the name of the projection images file
self.average_file = None # This is a string - the name of the class averages file
self.proj_class_viewer = None # This will be an EMImageMXWidget that shows the class and/or projection
self.particle_viewer = None # This will be an EMImageMXWidget that shows the particles in a class
self.clsdb = None # I think this will become redundant - it used to be the old database that stores which particles are in a class, but now that's stored in the header
self.particle_file = None # This will be a string - the name of the file that has the particle files in it. This might be made redundant with the new approach
self.alignment_file = None # This will be a string - the name of the file containing the alignment parameters - this is essential if you we want to show the aligned particles
self.refine_dir = None # This will be a string - the name of the current refinement directory that is being studied
self.dx = None # This is an EMData object storing the x shifts of the alignments for all particles. Generated by e2classaverage
self.dy = None # This is an EMData object storing the y shifts of the alignments for all particles. Generated by e2classaverage
self.da = None# This is an EMData object storing the angle of the alignments for all particles. Generated by e2classaverage
self.dflip = None # This is an EMData object storing whether or not tthe alignment involved a flip, for all particles. Generated by e2classaverage
self.classes = None # This is an EMData object storing which class(es) a particle belongs to. Generated by e2classaverage
self.inclusions = None # This is and EMDAta storing a boolean that indicates the particle was actually included in the final average. Generated by e2classaverage
self.average = None # This the class average itself, an EMData object
self.projection = None # This is the projection itelse, an EMData object
self.class_idx = None # This is the idx of the current class being studied in the interface
self.previous_len = -1 # To keep track of the number of class averages that were previously viewable. This helps to make sure we can switch to the same class average in the context of a different refinement iteration
self.mirror_eulers = False
if sparse_mode:
self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis
# Grab the symmetry from the workflow database if possible
sym = "c1"
if js_check_dict("refine_01/0_refine_parms.json"):
try: sym = str(js_open_dict("refine_01/0_refine_parms.json")["sym"])
except: pass
# Have to tell the EM3DSymModel that there is a new sym
self.set_symmetry(sym)
# this object will have
if self.au_data != None:
combo_entries = self.au_data.keys()
combo_entries.sort()
combo_entries.reverse()
if len(combo_entries) > 0:
au = combo_entries[0]
cls = self.au_data[au][0][0]
self.au_selected(au,cls)
self.mirror_eulers = True
self.init_lock = False
self.force_update=True # Force a display udpdate in EMImage3DSymModule
QtCore.QObject.connect(self, QtCore.SIGNAL("point_selected"), self.au_point_selected)
